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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.31

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-11-05, 04:31 CST based on data in:
        • /project/lbarreiro/USERS/austin/slamseq/data/fastp_reports
        • /project/lbarreiro/USERS/austin/slamseq/logs/hisat-3n/qc
        • /project/lbarreiro/USERS/austin/slamseq/data/featurecounts/nascent

        General Statistics

        Showing 40/40 rows and 7/12 columns.
        Sample NameAssignedAssigned% Aligned% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% AdapterMean R1 LengthMean R2 Length
        LB-HT-28s-HT-01_S1
        85.1%
        44.5%
        95.5%
        91267.3Mb
        625.6M
        47.0%
        98.5%
        18.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-01_S1_nascent
        2.3M
        26.7%
        LB-HT-28s-HT-02_S2
        84.8%
        38.0%
        94.8%
        81701.9Mb
        556.3M
        48.5%
        98.3%
        11.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-02_S2_nascent
        2.6M
        27.2%
        LB-HT-28s-HT-03_S3
        84.7%
        44.6%
        95.4%
        86741.3Mb
        590.6M
        47.3%
        98.5%
        14.8%
        158.0bp
        158.0bp
        LB-HT-28s-HT-03_S3_nascent
        2.6M
        30.3%
        LB-HT-28s-HT-05_S5
        82.9%
        41.5%
        92.8%
        72122.9Mb
        500.9M
        52.8%
        96.9%
        10.4%
        158.0bp
        158.0bp
        LB-HT-28s-HT-05_S5_nascent
        2.6M
        19.9%
        LB-HT-28s-HT-06_S6
        84.0%
        48.0%
        95.5%
        81205.9Mb
        558.3M
        46.1%
        98.5%
        21.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-06_S6_nascent
        1.8M
        25.5%
        LB-HT-28s-HT-07_S7
        84.1%
        49.0%
        95.0%
        90824.5Mb
        617.8M
        48.7%
        98.1%
        12.4%
        158.0bp
        158.0bp
        LB-HT-28s-HT-07_S7_nascent
        2.5M
        25.7%
        LB-HT-28s-HT-08_S8
        85.4%
        54.6%
        95.2%
        73660.6Mb
        498.1M
        48.2%
        98.0%
        10.8%
        158.0bp
        158.0bp
        LB-HT-28s-HT-08_S8_nascent
        2.0M
        26.7%
        LB-HT-28s-HT-09_S9
        83.7%
        43.1%
        93.6%
        91600.1Mb
        637.5M
        51.1%
        97.3%
        16.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-09_S9_nascent
        2.7M
        19.5%
        LB-HT-28s-HT-10_S10
        79.8%
        47.7%
        94.1%
        64392.3Mb
        436.1M
        49.7%
        97.7%
        4.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-10_S10_nascent
        1.6M
        19.2%
        LB-HT-28s-HT-12_S12
        80.0%
        36.3%
        94.6%
        67283.1Mb
        453.8M
        48.4%
        98.1%
        5.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-12_S12_nascent
        2.0M
        23.9%
        LB-HT-28s-HT-16_S16
        83.2%
        37.5%
        93.7%
        59116.6Mb
        404.1M
        51.2%
        97.4%
        7.7%
        158.0bp
        158.0bp
        LB-HT-28s-HT-16_S16_nascent
        1.7M
        19.9%
        LB-HT-28s-HT-17_S17
        50.0%
        0.0%
        68.2%
        0.0Mb
        0.0M
        57.7%
        14.7%
        0.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-18_S18
        82.3%
        39.3%
        93.8%
        56778.4Mb
        386.7M
        50.0%
        97.5%
        6.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-18_S18_nascent
        1.6M
        19.3%
        LB-HT-28s-JL-01_S19
        28.4%
        93.9%
        78380.6Mb
        545.3M
        50.7%
        97.7%
        14.5%
        158.0bp
        158.0bp
        LB-HT-28s-JL-02_S20
        88.2%
        39.0%
        95.6%
        77063.4Mb
        524.3M
        46.2%
        98.5%
        13.3%
        158.0bp
        158.0bp
        LB-HT-28s-JL-02_S20_nascent
        1.9M
        26.1%
        LB-HT-28s-JL-04_S22
        87.7%
        32.2%
        95.3%
        80983.8Mb
        554.5M
        47.8%
        98.5%
        14.3%
        158.0bp
        158.0bp
        LB-HT-28s-JL-04_S22_nascent
        2.4M
        24.0%
        LB-HT-28s-JL-05_S23
        87.1%
        57.3%
        94.7%
        66715.5Mb
        456.1M
        48.2%
        98.0%
        10.7%
        158.0bp
        158.0bp
        LB-HT-28s-JL-05_S23_nascent
        2.2M
        23.8%
        LB-HT-28s-JL-06_S24
        87.9%
        62.4%
        95.6%
        75404.5Mb
        522.6M
        46.9%
        98.1%
        18.6%
        158.0bp
        158.0bp
        LB-HT-28s-JL-06_S24_nascent
        1.9M
        25.0%
        LB-HT-28s-JL-07_S25
        87.3%
        54.4%
        95.0%
        95197.2Mb
        651.4M
        48.4%
        98.0%
        12.1%
        158.0bp
        158.0bp
        LB-HT-28s-JL-07_S25_nascent
        2.8M
        21.6%
        LB-HT-28s-JL-08_S26
        87.8%
        41.2%
        95.5%
        76972.6Mb
        524.7M
        46.2%
        98.6%
        13.2%
        158.0bp
        158.0bp
        LB-HT-28s-JL-08_S26_nascent
        2.0M
        25.9%
        LB-HT-28s-JL-09_S27
        88.1%
        51.9%
        95.6%
        96104.7Mb
        659.0M
        46.7%
        98.3%
        14.7%
        158.0bp
        158.0bp
        LB-HT-28s-JL-09_S27_nascent
        2.4M
        25.4%

        featureCounts

        Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.URL: http://subread.sourceforge.netDOI: 10.1093/bioinformatics/btt656

        Assignments

        Created with MultiQC

        HISAT2

        Maps DNA or RNA reads against a genome or a population of genomes.URL: https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        Created with MultiQC

        fastp

        Version: 1.0.1

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        fastp1.0.1

        MultiQC v1.31 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.